rm -rf ${maf_path}/All_ForMutBurden.MSI.maf
## colnums
## https://github.com/getzlab/MutSig2CV
## Start_Position需要替换为Start_position
cat ${maf_path}/*QC.maf | grep -m 1 Hugo_Symbol | sed 's/Start_Position/Start_position/' \
> ${maf_path}/All_ForMutBurden.MSI.maf
## 81为突变的reads数目，需保证有突变
for line in ` cat ${config_path}/tumor_normal.MSI.list | grep -v Normal | sort -u | tr '\t' ',' ` 
do
Tumor=`echo ${line} | awk -F, '{print $1}'`
Normal=`echo ${line} | awk -F, '{print $2}'`
maf_file=${maf_path}/${Tumor}_${Normal}_QC.maf
cat ${maf_file} | grep -v -E "##|Hugo_Symbol|#version" | awk -F'\t' '{OFS="\t"}{if($81>0){$16=Tumor;print}}' Tumor=${Tumor} \
>> ${maf_path}/All_ForMutBurden.MSI.maf
done

cat ${maf_path}/All_ForMutBurden.MSI.maf | \
awk -F'\t' '{OFS="\t"}{print $5,$6,$16,$11,$13,$1,$9,$10}' | head -1 > ${maf_path}/All_ForMutBurden.extract.MSI.maf
cat ${maf_path}/All_ForMutBurden.MSI.maf | grep -v Chromosome | \
awk -F'\t' '{OFS="\t"}{print $5,$6,$16,$11,$13,$1,$9,$10}' | sort -u >> ${maf_path}/All_ForMutBurden.extract.MSI.maf
